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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>Thank you very much Dr. McLaren.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>Just one clarification to the LRG choice. Is the LRG always presented as the first consequence (if it exists)? If this is true, then if the –-pick chooses the worst consequence, and there are multiple transcripts with the same “worst consequence”, does VEP --pick the first transcript with that consequence? If that is true, if the LRG contains the “worst consequence” along with other similar transcripts, will --pick successfully choose this consequence over other equal transcripts?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>Any help on this would be appreciated.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>Thank you again!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>Andrew<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>I should also say that there's currently no way to prioritise LRG<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>consequences other than filtering using filter_vep.pl, though this wouldn't<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>be a complete solution.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>Will<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>On 1 April 2014 09:51, Will McLaren <<a href="http://lists.ensembl.org/mailman/listinfo/dev">wm2 at ebi.ac.uk</a>> wrote:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> Hi Andrew,<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> In fact this is already possible; just add the flag --lrg at runtime. Note<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> however that using LRGs depends on connecting to our database, so this will<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> not work using --offline and will connect to ensembldb.ensembl.org when<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> using --cache. Because of this database connection you may find that the<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> script runs more slowly as it attempts to remap your input variants to LRG<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> coordinates.<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> I'm afraid this is missing from the documentation currently, I will get<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> that updated.<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> Regards<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> Will McLaren<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> Ensembl Variation<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i> On 31 March 2014 22:24, Andrew Carson <<a href="http://lists.ensembl.org/mailman/listinfo/dev">acarson at invivoscribe.com</a>> wrote:<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> Hi ensembl-dev team,<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> I was just wondering if there are plans to incorporate the LRG (locus<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> reference genomic) records into the VEP annotation pipeline (from here:<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> <a href="http://www.lrg-sequence.org/home">http://www.lrg-sequence.org/home</a>). I only ask because in the HGVS new<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> clinical reporting guidelines they recommend using the LRG sequence (if one<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> is present) to standardize variant reporting.<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> It would also be very useful to have an option where, if a variant<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> overlaps an LRG, you can choose to "pick" that consequence over other<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> consequences.<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> Any thoughts on if this could be added to the development for the next<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> release cycle?<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> Thanks for all of your help!<o:p></o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i><o:p> </o:p></i></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i> Andrew R. Carson, Ph.D.</i><o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p></div></body></html>